Add kraken2 pigz multi-tool container for compressing output fastq files (#434)

* Add kraken2 pigz multi-tool container for compressing output fastq files

* Add untar to pytest config

* Add untar process to kraken2 tests

* Remove unneeded tags

software/kraken2/run/main.nf

@@ -11,11 +11,11 @@ process KRAKEN2_RUN {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? 'bioconda::kraken2=2.1.1' : null)
+    conda (params.enable_conda ? 'bioconda::kraken2=2.1.1 conda-forge::pigz=2.6' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container 'https://depot.galaxyproject.org/singularity/kraken2:2.1.1--pl526hc9558a2_0'
+        container 'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:941789bd7fe00db16531c26de8bf3c5c985242a5-0'
     } else {
-        container 'quay.io/biocontainers/kraken2:2.1.1--pl526hc9558a2_0'
+        container 'quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:941789bd7fe00db16531c26de8bf3c5c985242a5-0'
     }
 
     input:
@@ -46,7 +46,8 @@ process KRAKEN2_RUN {
         $options.args \\
         $reads
 
-    gzip *.fastq
+    pigz -p $task.cpus *.fastq
+
     echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//' > ${software}.version.txt
     """
 }

tests/config/pytest_software.yml

@@ -307,6 +307,7 @@ kallistobustools/ref:
 
 kraken2/run:
   - software/kraken2/run/**
+  - software/untar/**
   - tests/software/kraken2/run/**
 
 mash/sketch:

tests/software/kraken2/run/main.nf

@@ -2,15 +2,17 @@
 
 nextflow.enable.dsl = 2
 
+include { UNTAR       } from '../../../../software/untar/main.nf'       addParams( options: [:] )
 include { KRAKEN2_RUN } from '../../../../software/kraken2/run/main.nf' addParams( options: [:] )
 
 workflow test_kraken2_run_single_end {
     input = [ [ id:'test', single_end:true ], // meta map
               [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
             ]
-    db    = file(params.test_data['sarscov2']['genome']['kraken2'], checkIfExists: true)
+    db    = file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true)
 
-    KRAKEN2_RUN ( input, db )
+    UNTAR ( db )
+    KRAKEN2_RUN ( input, UNTAR.out.untar )
 }
 
 workflow test_kraken2_run_paired_end {
@@ -18,7 +20,8 @@ workflow test_kraken2_run_paired_end {
               [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
                 file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
             ]
-    db    = file(params.test_data['sarscov2']['genome']['kraken2'], checkIfExists: true)
+    db    = file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true)
     
-    KRAKEN2_RUN ( input, db )
+    UNTAR ( db )
+    KRAKEN2_RUN ( input, UNTAR.out.untar )   
 }

tests/software/kraken2/run/test.yml

@@ -3,7 +3,6 @@
   tags:
     - kraken2
     - kraken2/run
-    - kraken2_run_single_end
   files:
     - path: output/kraken2/test.classified.fastq.gz
       should_exist: true
@@ -17,7 +16,6 @@
   tags:
     - kraken2
     - kraken2/run
-    - kraken2_run_paired_end
   files:
     - path: output/kraken2/test.classified_1.fastq.gz
       should_exist: true